git: 4724b7df2afd - main - biology/iolib: Update 1-15-1 => 1.16.0

The branch main has been updated by alven:

URL: https://cgit.FreeBSD.org/ports/commit/?id=4724b7df2afd47079b9f5137949d675ad7fa7a45

commit 4724b7df2afd47079b9f5137949d675ad7fa7a45
Author:     Älven <[email protected]>
AuthorDate: 2026-08-17 09:54:43 +0000
Commit:     Älven <[email protected]>
CommitDate: 2026-08-17 10:10:20 +0000

    biology/iolib: Update 1-15-1 => 1.16.0
    
    Approved by:            db@, yuri@ (Mentors, implicit)
---
 biology/iolib/Makefile                             | 12 +++++-----
 biology/iolib/distinfo                             |  6 ++---
 ...patch-htscodecs_htscodecs_rANS__static32x16pr.h | 11 ---------
 ...htscodecs_htscodecs_rANS__static32x16pr__neon.c | 11 ---------
 .../patch-htscodecs_htscodecs_rANS__static4x16pr.c | 11 ---------
 biology/iolib/pkg-plist                            | 26 ++--------------------
 biology/p5-Bio-SCF/Makefile                        |  2 +-
 7 files changed, 11 insertions(+), 68 deletions(-)

diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
index 37ef96698e30..ab7523fdf8ba 100644
--- a/biology/iolib/Makefile
+++ b/biology/iolib/Makefile
@@ -1,8 +1,8 @@
 PORTNAME=	io_lib
-DISTVERSION=	1-15-1
+DISTVERSION=	1.16.0
 CATEGORIES=	biology
 MASTER_SITES=	https://github.com/jkbonfield/${PORTNAME}/releases/download/${DISTNAME:S/./-/g}/
-DISTNAME=	${PORTNAME}-${PORTVERSION}
+DISTNAME=	${PORTNAME}-${DISTVERSION}
 
 MAINTAINER=	[email protected]
 COMMENT=	General purpose trace file (and Experiment File) reading interface
@@ -11,9 +11,10 @@ WWW=		https://staden.sourceforge.net/ \
 
 LICENSE=	BSD3CLAUSE
 
-LIB_DEPENDS=	libcurl.so:ftp/curl
+LIB_DEPENDS=	libcurl.so:ftp/curl \
+		libhts.so:biology/htslib
 
-USES=		autoreconf gmake libtool
+USES=		autoreconf gmake libtool localbase
 USE_LDCONFIG=	yes
 
 GNU_CONFIGURE=	yes
@@ -22,7 +23,4 @@ INSTALL_TARGET=	install-strip
 
 CONFLICTS_INSTALL=	filters scramble # bin/scramble
 
-pre-configure:
-	cd ${WRKSRC}/htscodecs && ${AUTORECONF} -f -i
-
 .include <bsd.port.mk>
diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo
index b7542b459186..ee953d074678 100644
--- a/biology/iolib/distinfo
+++ b/biology/iolib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1767736222
-SHA256 (io_lib-1.15.1.tar.gz) = 4e6f08265bee63211bb20feb4dc03993e57b447b90dc84a4c272cf1aed954e4f
-SIZE (io_lib-1.15.1.tar.gz) = 7357740
+TIMESTAMP = 1786958686
+SHA256 (io_lib-1.16.0.tar.gz) = db18f5ad2cc0c9ec0df4f14664df29362315fed13d8053dc24d00ef11e87d02a
+SIZE (io_lib-1.16.0.tar.gz) = 3644833
diff --git a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr.h b/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr.h
deleted file mode 100644
index 9794fb79ae06..000000000000
--- a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- htscodecs/htscodecs/rANS_static32x16pr.h.orig	2026-03-24 19:00:02 UTC
-+++ htscodecs/htscodecs/rANS_static32x16pr.h
-@@ -146,7 +146,7 @@ unsigned char *rans_uncompress_O1_32x16_avx512(unsigne
- 
- //----------------------------------------------------------------------
- // Arm Neon implementation
--#ifdef __ARM_NEON
-+#if defined(__ARM_NEON) && defined(__aarch64__)
- unsigned char *rans_compress_O0_32x16_neon(unsigned char *in,
-                                            unsigned int in_size,
-                                            unsigned char *out,
diff --git a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c b/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
deleted file mode 100644
index ad7cca53620c..000000000000
--- a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig	2026-03-24 19:00:35 UTC
-+++ htscodecs/htscodecs/rANS_static32x16pr_neon.c
-@@ -32,7 +32,7 @@
-  */
- 
- #include "config.h"
--#ifdef __ARM_NEON
-+#if defined(__ARM_NEON) && defined(__aarch64__)
- #include <arm_neon.h>
- 
- #include <limits.h>
diff --git a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c b/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
deleted file mode 100644
index 8cc3e85143ed..000000000000
--- a/biology/iolib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- htscodecs/htscodecs/rANS_static4x16pr.c.orig	2026-03-24 19:05:28 UTC
-+++ htscodecs/htscodecs/rANS_static4x16pr.c
-@@ -1006,7 +1006,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order)
-     }
- }
- 
--#elif defined(__ARM_NEON)
-+#elif defined(__ARM_NEON) && defined(__aarch64__)
- 
- #if defined(__linux__) || defined(__FreeBSD__)
- #include <sys/auxv.h>
diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
index 96dd5ca7cd49..940a9199f00d 100644
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -1,9 +1,5 @@
 bin/append_sff
 bin/convert_trace
-bin/cram_dump
-bin/cram_filter
-bin/cram_index
-bin/cram_size
 bin/extract_fastq
 bin/extract_qual
 bin/extract_seq
@@ -35,15 +31,6 @@ bin/srf_info
 bin/srf_list
 bin/trace_dump
 bin/ztr_dump
-include/htscodecs/arith_dynamic.h
-include/htscodecs/fqzcomp_qual.h
-include/htscodecs/htscodecs.h
-include/htscodecs/pack.h
-include/htscodecs/rANS_static.h
-include/htscodecs/rANS_static4x16.h
-include/htscodecs/rle.h
-include/htscodecs/tokenise_name3.h
-include/htscodecs/varint.h
 include/io_lib/Read.h
 include/io_lib/abi.h
 include/io_lib/alf.h
@@ -54,14 +41,6 @@ include/io_lib/binning.h
 include/io_lib/compress.h
 include/io_lib/compression.h
 include/io_lib/cram.h
-include/io_lib/cram_bambam.h
-include/io_lib/cram_codecs.h
-include/io_lib/cram_decode.h
-include/io_lib/cram_encode.h
-include/io_lib/cram_index.h
-include/io_lib/cram_io.h
-include/io_lib/cram_stats.h
-include/io_lib/cram_structs.h
 include/io_lib/deflate_interlaced.h
 include/io_lib/dstring.h
 include/io_lib/error.h
@@ -95,11 +74,10 @@ include/io_lib/vlen.h
 include/io_lib/xalloc.h
 include/io_lib/zfio.h
 include/io_lib/ztr.h
-lib/libhtscodecs.a
 lib/libstaden-read.a
 lib/libstaden-read.so
-lib/libstaden-read.so.14
-lib/libstaden-read.so.14.1.4
+lib/libstaden-read.so.16
+lib/libstaden-read.so.16.0.0
 share/man/man1/scramble.1.gz
 share/man/man1/srf2fasta.1.gz
 share/man/man1/srf2fastq.1.gz
diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile
index b56264f8a8cb..ec58d810dd6b 100644
--- a/biology/p5-Bio-SCF/Makefile
+++ b/biology/p5-Bio-SCF/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	Bio-SCF
 PORTVERSION=	1.03
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-